Go to Tools - Customize - Menus, click "Add command". The buttons "Add", "Close" and "Help" should be moved to the bottom.
Created attachment 132329 [details] move the dialog buttons to bottom +1
Some students showed interest in working on this dialog during GSoC'17. Basic idea is here https://user-prompt.com/de/how-to-make-libreoffice-customization-usable/
This is no longer a problem, since the Customize-Dialog has been redesigned. "Add command" is no longer a popup It's rather a split-view of available and already present options, where the user can simply add the commands he wants by sending them to the right. for reference: https://cgit.freedesktop.org/libreoffice/core/commit/?id=d69f9436b59e2